T. Piskackova

Genetic Structure of Europeans: A View from the North–East

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

A common variant on chromosome 11q13 is associated with atopic dermatitis.

We conducted a genome-wide association study in 939 individuals with atopic dermatitis and 975 controls as well as 270 complete nuclear families with two affected siblings. SNPs consistently associated with atopic dermatitis in both discovery sets were then investigated in two additional independent replication sets totalling 2,637 cases and 3,957 controls. Highly significant association was found with allele A of rs7927894 on chromosome 11q13.5, located 38 kb downstream of C11orf30 (Pcombined = 7.6 × 10−10). Approximately 13% of individuals of European origin are homozygous for rs7927894[A], and their risk of developing atopic dermatitis is 1.47 times that of noncarriers.

Association Screening in the Epidermal Differentiation Complex (EDC) Identifies an SPRR3 Repeat Number Variant as a Risk Factor for Eczema

The genetically determined impairment of the skin barrier is a primary cause of eczema. As numerous genes essential for an intact epidermis reside within the epidermal differentiation complex (EDC), we screened the National Center for Biotechnology Information (NCBI) database for putatively functional polymorphisms in the EDC genes and tested them for association with eczema. We identified 20 polymorphisms with predicted major impact on protein function. Of these, 4 were validated in 94 eczema patients: a nonsense mutation in FLG2 (rs12568784), a stop codon mutation in LCE1D (rs41268500), a 24-bp deletion in SPRR3 (rs28989168), and a frameshift mutation in S100A3 (rs11390146). The minor allele frequencies were 15.1, 6.1, 47.2, and 0.4%, respectively. Association testing of the validated polymorphisms in 555 eczema patients and 375 controls identified a significant effect of rs28989168 (SPRR3) on eczema. The association was replicated in another 1,314 cases and 1,322 controls, yielding an overall odds ratio of 1.30 (95% confidence interval 1.12-1.51; P=0.00067) for a dominant mode of inheritance. Small proline-rich proteins (SPRRs) are crossbridging proteins in the cornified cell envelope (CE), which provides the main barrier function of stratified squamous epithelia. The SPRR3 variant associated with eczema carried an extra 24-bp repeat in the central domain, which may alter the physical properties of the CE.

Pilot newborn screening project for cystic fibrosis in the Czech Republic: defining role of the delay in its symptomatic diagnosis and influence of ultrasound-based prenatal diagnosis on the incidence of the disease.

The objective need for cystic fibrosis (CF) newborn screening (NBS) in the Czech Republic has recently been substantiated by a significant delay of its symptomatic diagnosis. This trend most likely resulted from the process of decentralisation of health care which led to the deterioration of care for patients who need specialised approaches. Applied newborn screening model (IRT/DNA/IRT) was efficacious enough to detect CF cases with median age at diagnosis of 37 days. The incidence of CF (1 in 6946 live births) ascertained in this project was lower than that established previously by epidemiological studies (1 in 2700-1 in 3300). However, adjustment for broadly applied ultrasound-based prenatal diagnosis (PND) in the 2nd trimester of pregnancy, that was performed within the period of the project (1/2/2005-2/11/2006), rendered an incidence estimate of 1 in 4023. This value is closer to that observed in other CF NBS programmes and reflects influence of PND on the incidence of CF.

25 Cystic fibrosis (CF) prevalence derived from CF newborn screening (CFNBS) in the Czech Republic: comparison of previous epidemiological and current CFNBS-based disease prevalence data

Objectives: This study reviews parental views on how they were informed of the probable CF diagnosis, following neonatal screening, and explores which method parent’s found most acceptable. Methods: Retrospective questionnaires were used to find parents’ views on how they were told that their child had a probable diagnosis of CF, who told them initially, were they told at home or by the GP followed by hospital, how acceptable was the mode of information sharing? Results: 40 parents of children with CF were studied. Most parents (9 out of 12) who had been informed by their GP recall receiving inaccurate information about the condition. All parents (28 out of 28) who had received a home visit to be told about the CF diagnosis felt that the information received had been accurate and found it easier to accept. Conclusion: Our qualitative study confirms that parents who were given accurate information by CF professionals during a home visit found this an acceptable means of being informed of the probable diagnosis of CF. Parents reported less negative recollections of that time than parents who were informed by their GP and met CF professionals in hospital. We consider that this is a superior method of sharing the information about the diagnosis of CF.

17 Cystic fibrosis newborn screening (CF NBS): 4 year experience of the Prague Centre with the IRT/DNA/IRT protocol

Background: Cystic Fibrosis Newborn screening (CFNBS) as a pilot study started at the Institute of Mother and Child (IMC) Centre in 1999 and 444 063 newborns were examined until 2003. Current CFNBS has started gradually in Poland in 2006, covering the whole country in 2009 and is ongoing. 582 693 children were screened until the end of 2011. During CFNBS different protocol’s strategies were used. Aim: Impact of the implementation of NBS on the age of CF diagnosis. Methods: The study involved children diagnosed and treated only in IMC CF Centre (from 1999 until the end of 2011). Three groups were formed: 1. Pilot group (p-NBS) − 56 children, according to protocol strategy IRT/IRT and IRT/IRT/DNA, only F508del mutation was assessed; 2. Current group (c-NBS) − 92 children, IRT/IRT/DNA and IRT/DNA protocol, with expanded DNA analysis panel; 3. Patient diagnosed clinically (non-NBS) − 56 children. Moreover, DNA analysis in c-NBS group contains also frequent mutation in Polish population: 3849+10kbC>T, which is combined with low sweat test values. All patients underwent sweat tests. Results: The age of diagnosis was significantly lower (both p T than p-NBS and non-NBS group (both 0.9%). Conclusion: IRT/DNA strategy with extended DNA analysis provides an opportunity of earlier CF diagnosis even in children with normal sweat test values.